scBoolSeq notebooks

These notebooks demonstrate scBoolSeq for scRNA-Seq binarization and synthetic generation from Boolean dynamical models.

The notebooks can be visualized and downloaded at https://nbviewer.org/github/bnediction/scBoolSeq-supplementary.

Their execution require scBoolSeq installed (see https://github.com/bnediction/scBoolSeq#installation) and Python packages listed in the file requirements.txt. Alternatively, they can be executed interactively within the Docker image colomoto/scboolseq:v1, with the following command:

sudo python -m pip install -U colomoto-docker
colomoto-docker --image colomoto/scboolseq -V v1

⚠️ The notebooks 3.X - STREAM - ... and Variable Gene Selection ... must be executed within a STREAM environment (which is not included in the above mentioned Docker image). They can be be executed within the STREAM Docker distribution:

docker run --rm --entrypoint /usr/bin/env -v "$PWD/../:/data" -w /data -p 8989:8888 -it \
    pinellolab/stream:1.0 jupyter notebook --ip 0.0.0.0 --port 8888 --no-browser --allow-root \
    --NotebookApp.token=

Then go to http://127.0.0.1:8989